hello, I am using the obenergy program and GAFF force field to compute the
potential energy of some molecule, according to the following program
example:
obenergy -ff GAFF
/Users/Eric/Desktop/ExampleMolecules/GAFF-test-set/21208702.mol
according to forcefieldgaff.cpp, the energy is given by the s
Sorry again for the incessant emails - I just realized that some working
programs can be debugged even if .o files are missing. I was just entering
the commands wrong:
I can pass args to the gdb like this:
SYSTEM-PROCESSx32:bin Eric$ gdb --args obenergy -ff GAFF
/Users/Eric/Desktop/ExampleMolecul
Oops, I spoke too soon. Turns out that obenergy.cpp prints its promo
message correctly but I think I need to compile all of the .o object files
that get linked into obenergy as debuggable as well. I'm not sure how to
re-link the .o files though, because I get lots of errors like these:
warning: Co
Hello,
I haven't been able to get the XCode generator to work, but what I found is
that if I follow the standard build instructions using cmake:
mv openbabel-2.3.0 ob-src
mkdir ob-build
cd ob-build
cmake ../ob-src 2>&1 | tee cmake.out
make 2>&1 | tee make.out
I find that the executables are debu
Hello,
i try to execute this command on my joined.sdf File:
babel joined.sdf babelout.sdf -s"CNNNCNCNC" -at0.8
but this won't work. Every time i get only 1 molecule in my output but this
can't be.
I create the joined.sdf as follows: cat *.sdf > joined.txt and then mv
joined.txt joined.sdf
Ha
On 09/12/2011 19:44, Noel O'Boyle wrote:
> Or more succintly, with obabel 2.3.1 I have:
>
> C:\Users\Noel>obabel -:[Al]C#N -oinchi -xK -xX Recmet
> ==
> *** Open Babel Warning in InChI code
>#1 :Metal was disconnected
> ♥
> 1 molecule converted
>
> ...which is rathe
